ABIGAIL HOBBS is a tough character to sort because she is so impressionable, first molded by her father and later by Hannibal (and to a lesser extent, Freddie Lounds and Will). The Slytherin qualities she shows are unmistakable, but they seem to arise out of necessity rather than being intrinsic to who she is: she's self-preserving because she's had to be and cunning to the point of manipulation for the same reason. However, she feels guilty about surviving when the other girls didn't and lacks the ambition characteristic of a Slytherin.
Ultimately, Abigail fits best in Ravenclaw. She is quick-witted and intelligent: she knows what to do to get herself out of tough situations, and she realized immediately that it was Hannibal who called her father. She is clever, curious, and perceptive: she sees through people's ruses, and she is unafraid to ask probing questions. She is also fiercely independent and eager to learn, whether it's hunting with her father, cooking or playing the harpsichord with Hannibal, or fishing with Will. She belongs in Ravenclaw.
ALANA BLOOM is one of the characters who seems to change the most over the course of the show. In season 1, she is kind, idealistic, and naive; in season 2, she is conflicted as to who or what she should believe; and by season 3, she is a cold and calculating badass. However, it could be argued that who she is and what drives her doesn't really change; it's how that manifests itself that changes.
Like many people on the show, Alana adapts Slytherin traits as a coping mechanism and to keep herself and her family alive. But at her core, Alana is a Hufflepuff. She desires to help people, which is why she became a psychiatrist and a consultant for the FBI. She chooses to see the best in people, even when faced with damning evidence (e.g. with Will and Hannibal), and is loyal to a fault, sticking to her guns until she has no choice but to look truth in the face. She is compassionate, hardworking, and dedicated, and highly values loyalty, determination, and patience, which makes her a textbook Hufflepuff. Most importantly, she feels guilty when she hurts people or values her own self-preservation over others', which is her Hufflepuff core shining through in season 3.
BEDELIA DU MAURIER would be sorted into Slytherin. While she possesses a heavy dose of Ravenclaw curiosity, ultimately, her Slytherin traits win out. She is cunning enough to figure out who Hannibal is, to keep his interest without letting him too far into her head, and to get herself out of the sticky situation in Italy without being arrested or eaten. In fact, her strong sense of self-preservation keeps her from being harmed by Hannibal until the very end, when Will presumably had a say in the matter. She is slick and resourceful, twisting situations to suit her needs and talking in circles so as not to incriminate herself. She is also ambitious, although she has a tendency to get cold feet (for example, changing her mind in Italy once Hannibal started killing people in front of her), which is often her self-preservation overriding her more dangerous ambitions.
BEVERLY KATZ is one of the only true Gryffindor characters on the show. She has nerve and a strong sense of determination and courage. She wants to do what's right, even if it's difficult, which includes investigating Will when he's in prison. She also has a tendency to put herself on the front lines and rush into things without thinking, which ultimately leads to her demise.
BRIAN ZELLER may seem hard to sort, but he is without a doubt in Hufflepuff. What he values most is hard work and patience, which is why Will rubs him the wrong way when he waltzes into the forensics lab and makes conclusions without concrete evidence. Brian is diligent, dedicated, and loyal, as well, even if sometimes that means being loyal to the evidence and doing what is best for the community at large.
FREDDIE LOUNDS is the textbook definition of a Slytherin. She is cunning and resourceful, often several steps ahead of law enforcement and willing to do almost anything to get a good story. She is incredibly ambitious, clawing her way up from writing about phony cancer treatments in supermarket tabloids to running her own successful tabloid about crimes and serial killers, but she doesn't stop there — she sells t-shirts and other merchandise, and offers throughout the series to write books for or about other characters. She also has a strong sense of self-preservation, despite the dangerous situations that her job puts her in. After all, she's still standing at the end of the show, against all odds.
FREDERICK CHILTON is a Slytherin, although his Slytherin traits manifest differently than Freddie Lounds' or Bedelia's. Bedelia is cold, calculating, and cunning, seeing herself as superior to many of the characters she interacts with. Freddie is very ambitious and arguably more cunning than Bedelia, but without Bedelia's cold outward veneer and with a lot more spark. In comparison, Chilton holds Slytherin traits without being particularly good at them. He is ambitious, as the BSHCI administrator, and he desires to become famous through his notorious patients and books about criminal psychology. In reality, he has little luck with his patients, he was a shoddy surgeon, and his books are flops, but that never stops him. He is cunning, with his schemes, psychic driving, and salty quips and insults, even if they don't end up paying out. He is also determined and resourceful, and his self-preservation keeps him alive somehow after being disemboweled, shot in the face, and burned with his lips bitten off.
HANNIBAL LECTER is easy to mis-sort. The impulse for many people may be to put him in Slytherin. But although he shows textbook Slytherin traits (self-preservation, ambition, and cunning), these are more of tools for him to reach his true goals and passions than his natural state. He is willing to put these things on hold if need be (for example, turning himself in to the FBI, risking his security to make cannibal jokes or show his true self to Will, feeding his kills to unsuspecting guests, leaving murder tableaux everywhere...), so they are not ultimately what drives him.
Hannibal fits best in Ravenclaw precisely because he is driven by curiosity and a deep love of wisdom, art, and beauty. He collects hobbies as if they're knick-knacks: cooking, drawing, calligraphy, playing the harpsichord, hosting dinner parties, murdering people, going to the opera... He speaks multiple languages, including Lithuanian, Italian, English, and presumably Japanese, French, and Russian. He elevates his murders to an art, displaying them as Botticelli paintings or the diagram of the Wound Man. Heartfelt performances of music (or murder) can bring him to tears. But what solidifies his sorting is that he is unceasingly curious and embodies all the traits of a Ravenclaw: intelligence, sharpness, wit, creativity, originality, and individuality. After all, so much of what he does on the show is simply because he is "curious to see what would happen."
JACK CRAWFORD is the textbook definition of a Gryffindor. He is headstrong and stubborn and has an unbending set of morals — what's wrong is wrong and what's right is right, no exceptions. That means that no matter how much he may care about Will or Hannibal or anybody else in his life, if they turn out to be the "bad guys," they must be stopped. He is determined to catch his "villains," no matter the cost, which could mean sacrificing people (himself included) along the way. He is daring to the point of recklessness, arrogant in his self-righteousness, and has a hero complex, believing that it is his responsibility to fix the world and keep it running. Jack's traits are a double-edged sword: they enable him to get things done, and he is a well-respected leader, but he is also terrible at compromise and unbending when it would be better to be flexible. He is a Gryffindor at heart.
JIMMY PRICE would be right at home in Ravenclaw. He is passionate about forensic science, always shares interesting factoids during criminal investigations, and shows a love of random knowledge. From the little that we glean about Jimmy, he enjoys a wide variety of subjects; for example, he loves bees and is fascinated by and specializes in latent fingerprint analysis. He is clever, witty, sharp-tongued, and funny. (It's even possible that his struggles with alcohol are due to him always thinking too much and wanting to shut off his brain for a while, though that's pure speculation.)
MARGOT VERGER is a Slytherin through and through. Whether she would have landed in a different house given a different upbringing, it's hard to say, but there's no question about it in this reality. Margot is ambitious (she wants her brother dead because he's arguably the most evil character on the show, yes, but she would also like inherit the Verger estate and money), cunning, resourceful, determined, self-preserving, loyal to only a very select few, and even preoccupied with lineage, considering she wants to produce a male Verger heir. She rarely thinks about other people besides herself, but if you're on her good side, you're set for life.
MOLLY FOSTER GRAHAM is the textbook definition of a Hufflepuff. She has all the traditional Hufflepuff traits: hardworking, patient, loyal, determined, fair, modest, and kind. She is patient (she has to be, because Will is certainly not easy to deal with), determined to help whoever she can, intensely loyal, unflinchingly honest, and genuinely kind. And though we don't really get to see her hardworking nature in the show, in the book Red Dragon, she owns her own dress shop (and in all available source material, she is a hardworking mom, having been a single mother for who knows how many years).
REBA MCCLANE may seem hard to sort, but she fits best in Ravenclaw. She is fiercely independent, quick-witted and clever, sharp, and clearly intelligent. She enjoys teaching (she taught the blind for ten years before going into film development) and she eventually wants to go back to teaching, working with speech-and-hearing impaired children. She is touched by Dolarhyde's gesture of taking her to the zoo for a date, and calls it "elegant" and "eloquent," clearly enamored. She is also naturally curious, a perfect Ravenclaw combination.
WILL GRAHAM is the toughest character of them all to sort, not only because he changes and morphs so much over the show, but also because there are at least three major components to his decisions: what he wants to do, what he says he's going to do, and what he actually does. Often even Will doesn't know what he's going to do until he does it. Due to his enigmatic nature, the easiest way to sort him is to figure out what he is not.
For example, Will is not a Gryffindor. He shows Gryffindor's self-sacrificing tendencies (working himself to the bone for the FBI comes to mind) and wants to value a strong, unbending system of morals. However, he doesn't actually want to sacrifice himself (see: all the times he implicitly or explicitly asks Jack to quit, when he finally quits and marries Molly, when he puts Chilton in the line of fire instead of himself, etc.), and his morals are not unbending, as much as he may think they should be or wish they would be. As soon as Will or the people he cares about are in danger, he throws those morals away (see: not turning in Abigail or Hannibal after he figures out that Abigail killed Nicholas Boyle and Hannibal helped her bury the body; not turning in Hannibal after Mason's mutilation even though he told Jack he would report any incriminating evidence to him; nearly running away with Hannibal; setting up Chilton to be attacked by the Red Dragon to save himself; helping Hannibal escape prison; etc.).
Nor is Will in Slytherin. He, like many others on the show, adapts some Slytherin traits in order to better survive, but it isn't his natural state. Most importantly, he lacks the ambition and the strong sense of self-preservation inherent to Slytherins. He doesn't want to sacrifice himself, really, but in the end, he allows Jack to bulldoze over him and nearly dies from how hard he works himself, something that a Slytherin would not do. And Will is cunning, but in a way that leans more towards wit.
So is he a Ravenclaw? Not really. Sure, Will has wit and intelligence (he is a college professor and successful profiler, after all), but he lacks the driving curiosity of a Ravenclaw and doesn't prize learning or wisdom over all other qualities. He would rather fix boat motors and live in the middle of nowhere drinking whiskey with his dogs than pursue knowledge and wisdom.
That leaves Hufflepuff. On first glance, it may not seem to fit, but if you look closer, it makes perfect sense. Hufflepuffs aren't required to be friendly or sociable, after all. Will is hardworking and dedicated, often to the point of neglecting his health to solve a case. He is extremely patient (he has to be, as a good fisherman!), and he is diligent, paying attention to things and details that others overlook. He's modest, downplaying his strengths and abilities and actively disliking the attention that comes with notoriety. He is also loyal, even when it means having conflicted interests: he keeps Abigail's secret to protect her; values Hannibal's friendship and forgives him far past what a normal person would be comfortable with; tries to fulfill Jack's expectations even when he knows he'll fail; protects Alana even after she rejects him and outright believes he's a killer; cares about vulnerable people like Peter Bernadone, Georgia Madchen, Reba McClane, etc.; loves his dogs; the list goes on.
Will checks all the boxes, then, of a Hufflepuff: hard work, diligence and dedication, patience, loyalty, and modesty. He also cares about justice and morality, even when he goes astray. At the end of the day, Will is a vigilante, trying to do what is just even if his actions are not within the law (e.g. killing people). If bending those values is necessary to stay loyal to the people in his life (Hannibal especially), though, he will, even if he shows reluctance. Will Graham is a Hufflepuff through and through.
IN CONCLUSION...
GRYFFINDOR - Jack Crawford & Beverly Katz
HUFFLEPUFF - Will Graham, Alana Bloom, Brian Zeller, & Molly Foster Graham
RAVENCLAW - Hannibal Lecter, Abigail Hobbs, Jimmy Price, & Reba McClane
SLYTHERIN - Bedelia Du Maurier, Freddie Lounds, Frederick Chilton, & Margot Verger